Heteroptera species were collected from 48 sites distributed throughout the mainland and island complexes of Greece during 1999–2004. The aims of this study were to investigate Heteroptera distribution and abundance in Greek streams, identify the environmental factors that are linked to variation in their assemblages and to partition the influence of environmental and spatial components, alone and in combination, on Heteroptera community composition. Canonical ordination techniques (CCA) were used to determine the relationship between environmental variables and species abundance, while variation partitioning was performed using partial CCA to understand the importance of different explanatory variables in Heteroptera variation. Heteroptera variation was decomposed into independent and joint effects of local (physicochemical variables, microhabitat composition, stream width and depth), regional (land use/cover) and geographic variables (longitude, latitude, altitude and distance to source). Land use/cover, aquatic and riparian vegetation, stream size and water chemistry were the most important factors structuring Heteroptera assemblages. At regional scale, bug assemblages were mainly divided into those found in forested and agricultural landscapes, following water quality and microhabitat composition at local scale. Local variables accounted for 48% of the total explained variation, regional variables for 20% whereas geographical position appeared to be the least influencing factor (8.5%). The results of partial constraint analyses suggested that local variables play a major role in Heteroptera variation followed by regional variables.